[Gate-users] Gate on condor grid

[Alexandre Dupas]

Dear Albert,

I doubt that sourcing the script before launching the script on the
grid can work. Condor tends to launch the job in a clean environment
without retaining previously defined variables. You have to create a
small script that source the gate environment script and then launch
your Gate process.

We are running Gate on a condor grid with about 40 heterogeneous nodes
(MacOS, Linux X86_64, and Linux i686). For each machine, we have a
small configuration script which is executed before launching Gate in
condor mode. Here is some code sample you can adapt to your particular
needs.

#
OPENGATE_PATH="/mnt/nfs/OpenGate/gate-i686" # path where the i686
flavor of the libraries are built

# set gate configuration variables
export GATEHOME="${OPENGATE_PATH}/gate-devel" # gate install directory
export G4VERSION="9.1"
export G4INSTALL="${OPENGATE_PATH}/geant_4.9.1.p02"
export ROOTSYS="${OPENGATE_PATH}/root_5.26"
export ROOTLIB="${ROOTSYS}/lib"
export ECAT7_HOME="${OPENGATE_PATH}/ecat_7"
export LMF_HOME="${OPENGATE_PATH}/lmf_3.0"

# set path variables
export PATH="${ROOTSYS}/bin:${GATEHOME}/bin/Linux-g++:${PATH}"
export LD_LIBRARY_PATH="${ROOTLIB}:${OPENGATE_PATH}/clhep_2.0.3.2/lib"

# Gate environment
. "${GATEHOME}/env_gate.sh" # source the environment
#

The gate process is launched by a job.sh script which source the
previously defined script and execute Gate with the correct macro.

#!/bin/sh
#
HOSTNAME=`hostname`
GATE_ENV=/mnt/nfs/hosts/$HOSTNAME/config-gate.sh

JOB_NUMBER=$1 # the first parameter to the script is the job number

GATE_SCRIPT="job-$JOB_NUMBER.mac"

# source the environment
. "$GATE_ENV"

# launch Gate with the correct job
Gate $GATE_SCRIPT
#

And here is the `submit' variable that makes condor launching my
job.sh script with the correct parameter (job number) :

Executable = /path/to/job.sh
Arguments = $(Process)

I hope this can help you solve your issue.

Best regards,
Alexandre

--
Alexandre Dupas
Postodoctoral Research Fellow
INSERM U698, Bichat Médecine Nucléaire

2010/11/16 Albert Hirtl <albert.hirtl at meduniwien.ac.at>:
> Dear all,
>
> I am trying to get Gate running on a condor grid. When starting a simulation
> (which ran perfectly in non-grid-mode) I get the following error in the .err
> file:
>
> [G4-cerr] G4EMDataSet::FullFileName - G4LEDATA environment variable not set
> [G4-cerr]
> [G4-cerr] *** G4Exception: Aborting execution ***
>
> Is it not enough to execute "source env_gate.sh" in the shell before sending
> Gate to the grid? Do I have to set all variables that are set in the
> env_gate.sh globally in /etc/profile? Or am I on a completely wrong track?
>
> Any help would be very much appreciated!
>
> Cheers,
> Albert
>
> --
> Medizinische Universität Wien - Allgemeines Krankenhaus Wien
> Universitätsklinik für Nuklearmedizin
> Währinger Gürtel 18-20
> 1090 Wien
> Austria
>
> Tel.: +43 (0) 1 / 40400 5545
>
> Web: http://www.meduniwien.ac.at/user/albert.hirtl
>
>
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